You can use any timer app you like, but I use and recommend Seconds Pro.
It is easy to program and save your workouts to use in the future. It's available for iPhone and Android.
(You can also get the free version, but that one doesn't allow you to save the workouts, so you'll have to input them each time you do the workout.)
I generally use the "Circuit Timer" setting when inputting these workouts, because you can program the work/rest times easily for each move.
I've attached a free tutorial I made for how to use it.